From 71eb51833468d6072ee46f80d6109dacab7c47cf Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Feb 2015 17:24:48 +0100
Subject: [PATCH] Change to option types
---
.../sasc/biopet/pipelines/basty/Basty.scala | 2 +-
.../extensions/gatk/BaseRecalibrator.scala | 2 +-
.../biopet/extensions/gatk/GatkGeneral.scala | 4 +--
.../biopet/pipelines/gatk/GatkPipeline.scala | 3 +-
.../pipelines/gatk/GatkVariantcalling.scala | 3 --
.../core/BiopetCommandLineFunctionTrait.scala | 6 ++--
.../lumc/sasc/biopet/extensions/Bowtie.scala | 2 +-
.../sasc/biopet/extensions/Cutadapt.scala | 4 +--
.../lumc/sasc/biopet/extensions/Raxml.scala | 4 +--
.../sasc/biopet/extensions/RunGubbins.scala | 14 ++++-----
.../lumc/sasc/biopet/extensions/Sickle.scala | 4 +--
.../sasc/biopet/extensions/bwa/BwaMem.scala | 12 ++++----
.../extensions/macs2/Macs2CallPeak.scala | 20 +++++++------
.../extensions/picard/MarkDuplicates.scala | 12 ++++----
.../extensions/picard/MergeSamFiles.scala | 2 +-
.../biopet/extensions/picard/Picard.scala | 4 +--
.../biopet/extensions/picard/SamToFastq.scala | 4 +--
.../extensions/samtools/SamtoolsMpileup.scala | 2 +-
.../biopet/extensions/seqtk/SeqtkSeq.scala | 4 +--
.../sasc/biopet/pipelines/carp/Carp.scala | 8 ++---
.../pipelines/flexiprep/Flexiprep.scala | 27 +++++++++--------
.../biopet/pipelines/mapping/Mapping.scala | 14 ++++-----
.../sasc/biopet/pipelines/sage/Sage.scala | 30 +++++++++----------
23 files changed, 94 insertions(+), 93 deletions(-)
diff --git a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index c260f4561..f71dfefb7 100644
--- a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -124,7 +124,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val gubbins = new RunGubbins(this)
gubbins.fastafile = concensusVariants
- gubbins.startingTree = raxmlBi.getBipartitionsFile
+ gubbins.startingTree = Some(raxmlBi.getBipartitionsFile)
gubbins.outputDirectory = outputDir + dirSufixGubbins
add(gubbins)
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
index 3912958a5..c07a2a66c 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
@@ -12,7 +12,7 @@ class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.q
memoryLimit = Option(4)
override val defaultVmem = "8G"
- if (config.contains("scattercount")) scatterCount = config("scattercount")
+ if (config.contains("scattercount")) scatterCount = config("scattercount", default = 1)
if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").asString)
if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").asString)
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
index dc7cc5e40..147398ac7 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
@@ -19,7 +19,7 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
- reference_sequence = config("reference")
- gatk_key = config("gatk_key")
+ reference_sequence = config("reference", required = true)
+ if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 88600e576..0c8844790 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -36,7 +36,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var singleSampleCalling = config("single_sample_calling", default = true)
var reference: File = config("reference", required = true)
- var dbsnp: File = config("dbsnp")
var useAllelesOption: Boolean = config("use_alleles_option", default = false)
val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
@@ -72,7 +71,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
samToFastq.isIntermediate = true
qscript.add(samToFastq)
mapping.input_R1 = samToFastq.fastqR1
- mapping.input_R2 = samToFastq.fastqR2
+ mapping.input_R2 = Some(samToFastq.fastqR2)
mapping.init
mapping.biopetScript
addAll(mapping.functions) // Add functions of mapping to curent function pool
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 759181117..230eff772 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -32,9 +32,6 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
@Argument(doc = "Reference", shortName = "R", required = false)
var reference: File = config("reference", required = true)
- @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
- var dbsnp: File = config("dbsnp")
-
@Argument(doc = "OutputName", required = false)
var outputName: String = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 57c635935..91f156ac4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -38,7 +38,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
val defaultThreads = 1
@Argument(doc = "Vmem", required = false)
- var vmem: String = _
+ var vmem: Option[String] = None
val defaultVmem: String = ""
@Argument(doc = "Executable", required = false)
@@ -58,9 +58,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads)
- if (vmem == null) {
+ if (vmem.isEmpty) {
vmem = config("vmem")
- if (vmem == null && !defaultVmem.isEmpty) vmem = defaultVmem
+ if (vmem.isEmpty && !defaultVmem.isEmpty) vmem = Some(defaultVmem)
}
if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
jobName = configName + ":" + firstOutput.getName
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index 7f670a444..e192a845b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -43,7 +43,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8
var sam: Boolean = config("sam", default = true)
- var sam_RG: String = config("sam-RG")
+ var sam_RG: Option[String] = config("sam-RG")
var seedlen: Option[Int] = config("seedlen")
var seedmms: Option[Int] = config("seedmms")
var k: Option[Int] = config("k")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index ba145e2aa..e7a5a319e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -43,8 +43,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
if (config.contains("front")) for (adapter <- config("front").asList) opt_front += adapter.toString
var opt_discard: Boolean = config("discard", default = false)
- var opt_minimum_length: String = config("minimum_length", 1)
- var opt_maximum_length: String = config("maximum_length")
+ var opt_minimum_length: Option[Int] = config("minimum_length", 1)
+ var opt_maximum_length: Option[Int] = config("maximum_length")
def cmdLine = required(executable) +
// options
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index f73582371..4f6236179 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -60,11 +60,11 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
private var out: List[File] = Nil
var executableNonThreads: String = config("exe", default = "raxmlHPC")
- var executableThreads: String = config("exe_pthreads")
+ var executableThreads: Option[String] = config("exe_pthreads")
override def afterGraph {
if (threads == 0) threads = getThreads(defaultThreads)
- executable = if (threads > 1 && executableThreads != null) executableThreads else executableNonThreads
+ executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
super.afterGraph
out +:= getInfoFile
f match {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index 6c8892c9b..b87e3cb1e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
- var startingTree: File = config("starting_tree")
+ var startingTree: Option[File] = config("starting_tree")
@Input(doc = "Fasta file", shortName = "FQ")
var fastafile: File = _
@@ -36,21 +36,21 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var outputDirectory: String = _
executable = config("exe", default = "run_gubbins.py")
- var outgroup: String = config("outgroup")
- var filterPercentage: String = config("filter_percentage")
- var treeBuilder: String = config("tree_builder")
+ var outgroup: Option[String] = config("outgroup")
+ var filterPercentage: Option[String] = config("filter_percentage")
+ var treeBuilder: Option[String] = config("tree_builder")
var iterations: Option[Int] = config("iterations")
var minSnps: Option[Int] = config("min_snps")
- var convergeMethod: String = config("converge_method")
+ var convergeMethod: Option[String] = config("converge_method")
var useTimeStamp: Boolean = config("use_time_stamp", default = false)
- var prefix: String = config("prefix")
+ var prefix: Option[String] = config("prefix")
var verbose: Boolean = config("verbose", default = false)
var noCleanup: Boolean = config("no_cleanup", default = false)
override def afterGraph: Unit = {
super.afterGraph
jobLocalDir = new File(outputDirectory)
- if (prefix == null) prefix = fastafile.getName
+ if (prefix.isEmpty) prefix = Some(fastafile.getName)
val out: List[String] = List(".recombination_predictions.embl",
".recombination_predictions.gff",
".branch_base_reconstruction.embl",
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index 5c068b9ee..5056c70ab 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -43,7 +43,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
var fastqc: Fastqc = _
executable = config("exe", default = "sickle", freeVar = false)
- var qualityType: String = config("qualitytype")
+ var qualityType: Option[String] = config("qualitytype")
var qualityThreshold: Option[Int] = config("qualityThreshold")
var lengthThreshold: Option[Int] = config("lengthThreshold")
var noFiveprime: Boolean = config("noFiveprime", default = false)
@@ -54,7 +54,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --version"
override def afterGraph {
- if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
+ if (qualityType.isEmpty) qualityType = Some(defaultQualityType)
}
def cmdLine = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 09401898a..fc790b183 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -34,7 +34,7 @@ class BwaMem(val root: Configurable) extends Bwa {
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
- var R: String = config("R")
+ var R: Option[String] = config("R")
var k: Option[Int] = config("k")
var r: Option[Float] = config("r")
var S: Boolean = config("S", default = false)
@@ -49,11 +49,11 @@ class BwaMem(val root: Configurable) extends Bwa {
var e: Boolean = config("e", default = false)
var A: Option[Int] = config("A")
var B: Option[Int] = config("B")
- var O: String = config("O")
- var E: String = config("E")
- var L: String = config("L")
+ var O: Option[String] = config("O")
+ var E: Option[String] = config("E")
+ var L: Option[String] = config("L")
var U: Option[Int] = config("U")
- var x: String = config("x")
+ var x: Option[String] = config("x")
var p: Boolean = config("p", default = false)
var v: Option[Int] = config("v")
var T: Option[Int] = config("T")
@@ -61,7 +61,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var a: Boolean = config("a", default = false)
var C: Boolean = config("C", default = false)
var Y: Boolean = config("Y", default = false)
- var I: String = config("I")
+ var I: Option[String] = config("I")
override val defaultVmem = "6G"
override val defaultThreads = 8
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
index 0722e99a2..e6a9c48e9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
@@ -30,12 +30,12 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
@Output(doc = "Output file gappedPeak")
private var output_gapped: File = _
- var fileformat: String = config("fileformat")
+ var fileformat: Option[String] = config("fileformat")
var gsize: Option[Float] = config("gsize")
var keepdup: Boolean = config("keep-dup", default = false)
var buffersize: Option[Int] = config("buffer-size")
- var outputdir: String = config("outputDir")
- var name: String = config("name")
+ var outputdir: String = _
+ var name: Option[String] = config("name")
var bdg: Boolean = config("bdg", default = false)
var verbose: Boolean = config("verbose", default = false)
var tsize: Option[Int] = config("tsize")
@@ -56,12 +56,14 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var callsummits: Boolean = config("callsummits", default = false)
override def afterGraph: Unit = {
- output_narrow = new File(outputdir + name + ".narrowPeak")
- output_broad = new File(outputdir + name + ".broadPeak")
- output_xls = new File(outputdir + name + ".xls")
- output_bdg = new File(outputdir + name + ".bdg")
- output_r = new File(outputdir + name + ".r")
- output_gapped = new File(outputdir + name + ".gappedPeak")
+ if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
+ if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
+ output_narrow = new File(outputdir + name.get + ".narrowPeak")
+ output_broad = new File(outputdir + name.get + ".broadPeak")
+ output_xls = new File(outputdir + name.get + ".xls")
+ output_bdg = new File(outputdir + name.get + ".bdg")
+ output_r = new File(outputdir + name.get + ".r")
+ output_gapped = new File(outputdir + name.get + ".gappedPeak")
}
def cmdLine = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index f88304a0a..6df04c12c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -32,19 +32,19 @@ class MarkDuplicates(val root: Configurable) extends Picard {
var outputMetrics: File = _
@Argument(doc = "PROGRAM_RECORD_ID", required = false)
- var programRecordId: String = config("programrecordid")
+ var programRecordId: Option[String] = config("programrecordid")
@Argument(doc = "PROGRAM_GROUP_VERSION", required = false)
- var programGroupVersion: String = config("programgroupversion")
+ var programGroupVersion: Option[String] = config("programgroupversion")
@Argument(doc = "PROGRAM_GROUP_COMMAND_LINE", required = false)
- var programGroupCommandLine: String = config("programgroupcommandline")
+ var programGroupCommandLine: Option[String] = config("programgroupcommandline")
@Argument(doc = "PROGRAM_GROUP_NAME", required = false)
- var programGroupName: String = config("programgroupname")
+ var programGroupName: Option[String] = config("programgroupname")
@Argument(doc = "COMMENT", required = false)
- var comment: String = config("comment")
+ var comment: Option[String] = config("comment")
@Argument(doc = "REMOVE_DUPLICATES", required = false)
var removeDuplicates: Boolean = config("removeduplicates", default = false)
@@ -62,7 +62,7 @@ class MarkDuplicates(val root: Configurable) extends Picard {
var sortingCollectionSizeRatio: Option[Double] = config("sortingCollectionSizeRatio")
@Argument(doc = "READ_NAME_REGEX", required = false)
- var readNameRegex: String = config("readNameRegex")
+ var readNameRegex: Option[String] = config("readNameRegex")
@Argument(doc = "OPTICAL_DUPLICATE_PIXEL_DISTANCE", required = false)
var opticalDuplicatePixelDistance: Option[Int] = config("opticalDuplicatePixelDistance")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
index b1327bc3a..4de143498 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
@@ -41,7 +41,7 @@ class MergeSamFiles(val root: Configurable) extends Picard {
var useThreading: Boolean = config("use_threading", default = false)
@Argument(doc = "COMMENT", required = false)
- var comment: String = config("comment")
+ var comment: Option[String] = config("comment")
override def commandLine = super.commandLine +
repeat("INPUT=", input, spaceSeparated = false) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index cc571ca7d..e417a85fd 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -22,13 +22,13 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
override def subPath = "picard" :: super.subPath
@Argument(doc = "VERBOSITY", required = false)
- var verbosity: String = config("verbosity")
+ var verbosity: Option[String] = config("verbosity")
@Argument(doc = "QUIET", required = false)
var quiet: Boolean = config("quiet", default = false)
@Argument(doc = "VALIDATION_STRINGENCY", required = false)
- var stringency: String = config("validationstringency")
+ var stringency: Option[String] = config("validationstringency")
@Argument(doc = "COMPRESSION_LEVEL", required = false)
var compression: Option[Int] = config("compressionlevel")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index cb61cc4a8..db784ee2b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -38,7 +38,7 @@ class SamToFastq(val root: Configurable) extends Picard {
var outputPerRg: Boolean = config("outputPerRg", default = false)
@Argument(doc = "Output dir", required = false)
- var outputDir: String = config("outputDir")
+ var outputDir: String = _
@Argument(doc = "re reverse", required = false)
var reReverse: Boolean = config("reReverse", default = false)
@@ -53,7 +53,7 @@ class SamToFastq(val root: Configurable) extends Picard {
var clippingAtribute: String = config("clippingAtribute")
@Argument(doc = "clippingAction", required = false)
- var clippingAction: String = config("clippingAction")
+ var clippingAction: Option[String] = config("clippingAction")
@Argument(doc = "read1Trim", required = false)
var read1Trim: Option[Int] = config("read1Trim")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
index f0e6457a4..b8a3a2d0e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
@@ -30,7 +30,7 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
var reference: File = config("reference")
@Input(doc = "Interval bed")
- var intervalBed: File = config("interval_bed")
+ var intervalBed: Option[File] = config("interval_bed")
var disableBaq: Boolean = config("disable_baq")
var minMapQuality: Option[Int] = config("min_map_quality")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
index be42104c0..9838040cc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
@@ -37,7 +37,7 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
var q: Option[Int] = config("q")
/** masked bases converted to CHAR; 0 for lowercase [0] */
- var n: String = config("n")
+ var n: Option[String] = config("n")
/** number of residues per line; 0 for 2^32-1 [0] */
var l: Option[Int] = config("l")
@@ -52,7 +52,7 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
var f: Option[Int] = config("f")
/** mask regions in BED or name list FILE [null] */
- var M: File = config("M")
+ var M: Option[File] = config("M")
/** drop sequences with length shorter than INT [0] */
var L: Option[Int] = config("L")
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index b06c01f57..f0ff3f4eb 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -86,8 +86,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
val macs2 = new Macs2CallPeak(qscript)
macs2.treatment = bamFile
- macs2.name = sampleId
- macs2.outputdir = sampleDir + "macs2/" + macs2.name + "/"
+ macs2.name = Some(sampleId)
+ macs2.outputdir = sampleDir + "macs2/" + sampleId + "/"
add(macs2)
}
}
@@ -113,8 +113,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
val macs2 = new Macs2CallPeak(this)
macs2.treatment = sample.bamFile
macs2.control = samples(controlId).bamFile
- macs2.name = sampleId + "_VS_" + controlId
- macs2.outputdir = sample.sampleDir + "/" + "macs2/" + macs2.name + "/"
+ macs2.name = Some(sampleId + "_VS_" + controlId)
+ macs2.outputdir = sample.sampleDir + "/" + "macs2/" + macs2.name.get + "/"
add(macs2)
}
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index db5c638fd..42ea3b6d9 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -30,7 +30,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var input_R1: File = _
@Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
- var input_R2: File = _
+ var input_R2: Option[File] = _
/** Skip Trim fastq files */
var skipTrim: Boolean = config("skip_trim", default = false)
@@ -63,7 +63,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if (sampleId == null) throw new IllegalStateException("Missing Sample name on flexiprep module")
if (libraryId == null) throw new IllegalStateException("Missing Library name on flexiprep module")
else if (!outputDir.endsWith("/")) outputDir += "/"
- paired = (input_R2 != null)
if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
@@ -71,12 +70,16 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
R1_ext = R1_name.substring(R1_name.lastIndexOf("."), R1_name.size)
R1_name = R1_name.substring(0, R1_name.lastIndexOf(R1_ext))
- if (paired) {
- if (input_R2.endsWith(".gz")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gz"))
- else if (input_R2.endsWith(".gzip")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gzip"))
- else R2_name = input_R2.getName
- R2_ext = R2_name.substring(R2_name.lastIndexOf("."), R2_name.size)
- R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
+ input_R2 match {
+ case Some(fileR2) => {
+ paired = true
+ if (fileR2.endsWith(".gz")) R2_name = fileR2.getName.substring(0, fileR2.getName.lastIndexOf(".gz"))
+ else if (fileR2.endsWith(".gzip")) R2_name = fileR2.getName.substring(0, fileR2.getName.lastIndexOf(".gzip"))
+ else R2_name = fileR2.getName
+ R2_ext = R2_name.substring(R2_name.lastIndexOf("."), R2_name.size)
+ R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
+ }
+ case _ =>
}
summary.out = outputDir + sampleId + "-" + libraryId + ".qc.summary.json"
@@ -95,7 +98,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
def runInitialJobs() {
outputFiles += ("fastq_input_R1" -> extractIfNeeded(input_R1, outputDir))
- if (paired) outputFiles += ("fastq_input_R2" -> extractIfNeeded(input_R2, outputDir))
+ if (paired) outputFiles += ("fastq_input_R2" -> extractIfNeeded(input_R2.get, outputDir))
fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
add(fastqc_R1)
@@ -107,12 +110,12 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
summary.addMd5sum(md5sum_R1, R2 = false, after = false)
if (paired) {
- fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
+ fastqc_R2 = Fastqc(this, input_R2.get, outputDir + "/" + R2_name + ".fastqc/")
add(fastqc_R2)
summary.addFastqc(fastqc_R2, R2 = true)
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
- val md5sum_R2 = Md5sum(this, input_R2, outputDir)
+ val md5sum_R2 = Md5sum(this, input_R2.get, outputDir)
add(md5sum_R2)
summary.addMd5sum(md5sum_R2, R2 = true, after = false)
}
@@ -278,7 +281,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
add(zcatCommand)
return newFile
} else if (file.getName().endsWith(".bz2")) {
- var newFile = swapExt(runDir, file, ".bz2", "")
+ val newFile = swapExt(runDir, file, ".bz2", "")
val pbzip2 = Pbzip2(this, file, newFile)
pbzip2.isIntermediate = true
add(pbzip2)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 7ed86a669..e1080ff0f 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -36,7 +36,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var input_R1: File = _
@Input(doc = "R2 fastq file", shortName = "R2", required = false)
- var input_R2: File = _
+ var input_R2: Option[File] = None
/** Output name */
var outputName: String = _
@@ -98,7 +98,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
else if (!outputDir.endsWith("/")) outputDir += "/"
if (input_R1 == null) throw new IllegalStateException("Missing FastQ R1 on mapping module")
- paired = (input_R2 != null)
+ paired = input_R2.isDefined
if (libraryId == null) libraryId = config("library_id")
if (sampleId == null) sampleId = config("sample_id")
@@ -125,7 +125,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if (!skipFlexiprep) {
flexiprep.outputDir = outputDir + "flexiprep" + File.separator
flexiprep.input_R1 = input_R1
- if (paired) flexiprep.input_R2 = input_R2
+ flexiprep.input_R2 = input_R2
flexiprep.sampleId = this.sampleId
flexiprep.libraryId = this.libraryId
flexiprep.init
@@ -144,10 +144,10 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) {
val chunkDir = outputDir + "chunks/" + t + "/"
chunks += (chunkDir -> (removeGz(chunkDir + input_R1.getName),
- if (paired) removeGz(chunkDir + input_R2.getName) else ""))
+ if (paired) removeGz(chunkDir + input_R2.get.getName) else ""))
}
else chunks += (outputDir -> (flexiprep.extractIfNeeded(input_R1, flexiprep.outputDir),
- flexiprep.extractIfNeeded(input_R2, flexiprep.outputDir)))
+ flexiprep.extractIfNeeded(input_R2.getOrElse(null), flexiprep.outputDir)))
if (chunking) {
val fastSplitter_R1 = new FastqSplitter(this)
@@ -158,7 +158,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if (paired) {
val fastSplitter_R2 = new FastqSplitter(this)
- fastSplitter_R2.input = input_R2
+ fastSplitter_R2.input = input_R2.get
for ((chunkDir, fastqfile) <- chunks) fastSplitter_R2.output :+= fastqfile._2
fastSplitter_R2.isIntermediate = true
add(fastSplitter_R2)
@@ -265,7 +265,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaCommand.R1 = R1
if (paired) bwaCommand.R2 = R2
bwaCommand.deps = deps
- bwaCommand.R = getReadGroup
+ bwaCommand.R = Some(getReadGroup)
bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
bwaCommand.isIntermediate = true
add(bwaCommand)
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 03be2ded6..c8b5c7030 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -35,13 +35,13 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
qscript =>
def this() = this(null)
- var countBed: File = config("count_bed")
+ var countBed: Option[File] = config("count_bed")
- var squishedCountBed: File = config("squished_count_bed")
+ var squishedCountBed: Option[File] = config("squished_count_bed")
- var transcriptome: File = config("transcriptome")
+ var transcriptome: Option[File] = config("transcriptome")
- var tagsLibrary: File = config("tags_library")
+ var tagsLibrary: Option[File] = config("tags_library")
override def defaults = ConfigUtils.mergeMaps(Map("bowtie" -> Map(
"m" -> 1,
@@ -127,28 +127,28 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def init() {
if (!outputDir.endsWith("/")) outputDir += "/"
- if (transcriptome == null && tagsLibrary == null)
+ if (transcriptome.isEmpty && tagsLibrary.isEmpty)
throw new IllegalStateException("No transcriptome or taglib found")
if (countBed == null && squishedCountBed == null)
throw new IllegalStateException("No bedfile supplied, please add a countBed or squishedCountBed")
}
def biopetScript() {
- if (squishedCountBed == null) {
- val squishBed = SquishBed(this, countBed, outputDir)
+ if (squishedCountBed.isEmpty) {
+ val squishBed = SquishBed(this, countBed.get, outputDir)
add(squishBed)
- squishedCountBed = squishBed.output
+ squishedCountBed = Some(squishBed.output)
}
- if (tagsLibrary == null) {
+ if (tagsLibrary.isEmpty) {
val cdl = new SageCreateLibrary(this)
- cdl.input = transcriptome
+ cdl.input = transcriptome.get
cdl.output = outputDir + "taglib/tag.lib"
cdl.noAntiTagsOutput = outputDir + "taglib/no_antisense_genes.txt"
cdl.noTagsOutput = outputDir + "taglib/no_sense_genes.txt"
cdl.allGenesOutput = outputDir + "taglib/all_genes.txt"
add(cdl)
- tagsLibrary = cdl.output
+ tagsLibrary = Some(cdl.output)
}
addSamplesJobs()
@@ -158,19 +158,19 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: String) {
- val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.sense.coverage",
+ val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.sense.coverage",
depth = false, sameStrand = true, diffStrand = false)
val countSense = new BedtoolsCoverageToCounts(this)
countSense.input = bedtoolsSense.output
countSense.output = outputDir + outputPrefix + ".genome.sense.counts"
- val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.antisense.coverage",
+ val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.antisense.coverage",
depth = false, sameStrand = false, diffStrand = true)
val countAntisense = new BedtoolsCoverageToCounts(this)
countAntisense.input = bedtoolsAntisense.output
countAntisense.output = outputDir + outputPrefix + ".genome.antisense.counts"
- val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.coverage",
+ val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.coverage",
depth = false, sameStrand = false, diffStrand = false)
val count = new BedtoolsCoverageToCounts(this)
count.input = bedtools.output
@@ -187,7 +187,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
val createTagCounts = new SageCreateTagCounts(this)
createTagCounts.input = countFastq.output
- createTagCounts.tagLib = tagsLibrary
+ createTagCounts.tagLib = tagsLibrary.get
createTagCounts.countSense = outputDir + outputPrefix + ".tagcount.sense.counts"
createTagCounts.countAllSense = outputDir + outputPrefix + ".tagcount.all.sense.counts"
createTagCounts.countAntiSense = outputDir + outputPrefix + ".tagcount.antisense.counts"
--
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